Align The glucose uptake porter, GluP (characterized)
to candidate WP_083709761.1 BW971_RS11095 sugar porter family MFS transporter
Query= TCDB::Q0SE66 (483 letters) >NCBI__GCF_900156495.1:WP_083709761.1 Length = 504 Score = 458 bits (1178), Expect = e-133 Identities = 236/454 (51%), Positives = 317/454 (69%), Gaps = 7/454 (1%) Query: 26 IAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASALLGAAAGAMLAGRIAD 85 + V AA+GG LFG+DS+V+NGAV +I+G F + + GFA+A ALLG A GA AGR+AD Sbjct: 44 VTVAAAVGGFLFGFDSSVVNGAVDSIKGHFALSEFVTGFAVAIALLGCAVGAWFAGRLAD 103 Query: 86 RYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIAEISPAR 145 +GR M +++F+ S+IGT F ++ L+ +R++GG+G+G+ASVIAPAYIAEI+PAR Sbjct: 104 VWGRKRVMLLGSLLFVASSIGTAFCFSLGDLLFWRVLGGLGIGIASVIAPAYIAEIAPAR 163 Query: 146 VRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEAWRWMFLAMCVPALAYG 205 RG LGSLQQLAI GIF++LL D L AG + LW G+EAWRWMFL +PA+ YG Sbjct: 164 FRGALGSLQQLAITIGIFIALLSDSLLQDSAGAAANTLWLGVEAWRWMFLVGVIPAVIYG 223 Query: 206 LLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSIRDLKGS 265 +L+L IPESPRYL+ EA IL + GE+ +++ IR TL RE++ SIRD++G Sbjct: 224 VLALLIPESPRYLVGNHLDEEAARILTEVTGEQNPLERVKEIRLTLVRESKASIRDIRGP 283 Query: 266 AFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVVNIATTL 325 +FGL P VW+GI L+VFQQFVGIN IFYYS+ LW +VGF E S + +VIT+V+N+ T Sbjct: 284 SFGLHPFVWVGIWLAVFQQFVGINAIFYYSTTLWSSVGFSESDSFKTSVITAVINVVMTF 343 Query: 326 IAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQGPIALVA 385 +I ++DR GRR +L+IGS GM V L +A + T D +T P G+ IAL+ Sbjct: 344 GSILFVDRFGRRRMLLIGSVGMFVGL-LLACVAFTQQIGSGDKITLPDPWGV---IALIG 399 Query: 386 ANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSMKDFSLG 445 ANLFV+AF +WGP++WV+LGE FPNR+R AL + A W AN+ IT+ FP + S+G Sbjct: 400 ANLFVIAFAATWGPILWVMLGEMFPNRLRGVALGVCTAANWVANFAITLLFPELNS-SIG 458 Query: 446 IS--YGFYAVCAVLSLVFVLRWVKETKGVELEAM 477 ++ YGF+A CA S +FV V ETKG+ELEAM Sbjct: 459 LAWIYGFFAFCAAASFLFVQFKVPETKGMELEAM 492 Lambda K H 0.324 0.138 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 731 Number of extensions: 37 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 483 Length of database: 504 Length adjustment: 34 Effective length of query: 449 Effective length of database: 470 Effective search space: 211030 Effective search space used: 211030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory